2P51

Crystal structure of the S. pombe Pop2p deadenylation subunit


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529318-24% PEG 8000, 200 mM Mg(CH3COO), 100-200 mM MES, pH 6.5, 0-10% glycerol, 5 mM BME, 1mM NaN3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
6.926228

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.37α = 90
b = 54.089β = 90
c = 90.959γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmBent, vertically focussing mirrors2005-03-10MSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8126EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.446.4799.60.05226.74.7508565085617.311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4299.70.6361.984.22489

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT1.446.475085650856152399.60.1430.1410.1390.204RANDOM23.937
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
s_from_restr_planes0.359
s_non_zero_chiral_vol0.066
s_angle_d0.03
s_anti_bump_dis_restr0.015
s_bond_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2084
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
SHELXrefinement
PDB_EXTRACTdata extraction
SHELXL-97refinement